How to query and download the WGS and gene expression data from paired solid Normal and solid Tumor samples in TCGA database?

Question

[lazyplant]

I think this might be an easy question for some people, But I have stuck on this problem for a whole day. I need to download whole genome sequencing and gene expression data(counts of reads at each genes) from matched normal tissue and tumor tissue of the same patient. such as this figure in my dropbox.

I pocked around at GDC legacy Archive and can not figure out what are the relations among the files in a same case. I think I need more time to familiar with GDC data structure. Thanks!

[fanli.gcb]

Have you tried http://www.cbioportal.org/?

[fr]

You may want to have a look at this answer to a very similar question that I asked.

Answer 1

[pxf109]

The TCGAbiolinks is a very useful tool for you. You can absolutely get the gene expression data through that. I am not sure whether you can get whole genome data, some data is not open for everyone.